This one is definitely worth a read for phylogeneticists and phylogenomicists (is that a word?) out there: PLoS Biology: Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough. Philippe et al. discuss some important issues in using genomes to infer phylogenies of species in this commentary/review paper. They discuss in particular some recent studies of animal evolution but they cover a lot of useful ground here and include a good review of terminology and some of the basic issues at play. I am personally going to have to read it in more detail to help deal with some of the issues in our recent study of novel sequences in metagenomic data.